LOD = 0.0 at all theta ???!!!

wijsman at max.u.washington.edu wijsman at max.u.washington.edu
Tue Nov 16 14:09:35 EST 1993


>   I have just run a 2 point linkage on a 60-member family, with disease
> plus 1 four-allele marker, on LINKAGE 5.2 on a Sun. The data was very
> informative, with perfect linkage.
>   MLINK with theta from 0-0.5 (inc = 0.05) gave LOD 0.0 at _all_ values!!
>   LODSCORE also gives LOD of 0.=.
> 
>   Our configuration usually works, but I have not run "bigger" than about
> individuals before. Any ideas where the problem (bug?) lies?.

I don't use Suns, so I can only guess at the source of your problem,
but my two guesses are (1) there is some problem with your data (have
you run a dummy simple 2-allele marker on the same pedigree to make
sure that works?), or (2) you are running into an underflow problem
(try boosting the scale parameter WAY up - perhaps 10.0 to 15.0).

Ellen Wijsman
Div of Medical Genetics, RG-25
and Dept of Biostatistics
University of Washington
Seattle, WA   98195
wijsman at u.washington.edu



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